How to use the genomepy.utils function in genomepy

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github vanheeringen-lab / genomepy / tests / test_04_download_annotation.py View on Github external
def test_ensemblgenomes_annotation(localname=None):
    """Test Ensembl annotation

    This annotation is hosted on ftp.ensemblgenomes.org.
    """
    tmp = mkdtemp()
    p = genomepy.provider.ProviderBase.create("Ensembl")

    for name, version in [("TAIR10", 45)]:
        p.download_annotation(name, tmp, localname=localname, version=version)

        localname = genomepy.utils.get_localname(name, localname)
        gtf = os.path.join(tmp, localname, localname + ".annotation.gtf.gz")
        validate_gzipped_gtf(gtf)

        bed = os.path.join(tmp, localname, localname + ".annotation.bed.gz")
        validate_gzipped_bed(bed)

    shutil.rmtree(tmp)
github vanheeringen-lab / genomepy / tests / test_5_install_options.py View on Github external
def test_install_annotation_options(
    force, localname, annotation=True, genome="ASM14646v1", provider="NCBI"
):
    """Test force and localname with annotations"""
    tmp = mkdtemp()
    force = False if force == "no-overwrite" else True
    localname = None if localname == "original_name" else "My_localname"

    # create dummy fasta to skip download_genome step
    name = genomepy.utils.get_localname(genome, localname)
    path = os.path.join(tmp, name, name + ".fa")
    os.mkdir(os.path.dirname(path))
    with open(path, "w") as f:
        f.write(">Chr1\nAAAACCCCTTTTGGGG\n")
    genomepy.install_genome(
        genome,
        provider,
        genome_dir=tmp,
        localname=localname,
        annotation=annotation,
        force=False,
    )

    gtf = os.path.join(tmp, name, name + ".annotation.gtf.gz")
    validate_gzipped_gtf(gtf)
github vanheeringen-lab / genomepy / tests / test_5_install_options.py View on Github external
def test_install_genome_options(
    force, localname, bgzip, genome="ASM2732v1", provider="NCBI"
):
    """Test force, localname and bgzip"""
    tmp = mkdtemp()
    force = False if force == "no-overwrite" else True
    localname = None if localname == "original_name" else "My_localname"
    bgzip = False if bgzip == "unzipped" else True

    genomepy.install_genome(
        genome, provider, genome_dir=tmp, localname=localname, bgzip=bgzip, force=force
    )

    # force test
    ext = ".fa.gz" if bgzip else ".fa"
    name = genomepy.utils.get_localname(genome, localname)
    path = os.path.join(tmp, name, name + ext)

    t0 = os.path.getmtime(path)
    # OSX rounds down getmtime to the second
    if system() != "Linux":
        sleep(1)
    genomepy.install_genome(
        genome, provider, genome_dir=tmp, localname=localname, bgzip=bgzip, force=force
    )

    t1 = os.path.getmtime(path)
    assert t0 != t1 if force else t0 == t1

    shutil.rmtree(tmp)